Revelations from Patch 7.2: Seekers of Eternity

[Cleretic]

You give Preservation's other members a lot of credit, even though it is safe to say that Calyx as an individual has been in complete control of Alexandria for hundreds of years. (Control he loaned out to Endless Sphene, for a mere experiment)
If what Simulant Sphene says represents Calyx' opinion of Sphene, he really doesn't think highly of her beyond her ability to control the masses. And he thinks even less of her people, treating them like lab rats. I don't recognize a sense of duty to his queen anywhere.
Could he have simply ignored Sphene's real body being frozen in the middle of the most important structure of "his" Everkeep? Possible, but it doesn't sit right with me.

I think you're looking at Preservation (which I did confuse with Oblivion! I blame Bethesda) and Calyx differently than I am, at least. You definitely seem to be looking at him as on some level actively malevolent, someone who would kill an innocent Sphene, more or less, because he can; after all, she's harmless and inert, and merely costs one extra room in the Meso Terminal. That she's useless, and you throw away things that are useless.

I'm looking at Preservation and Calyx as, while essentially antagonistic and evil by story requirement, above all else people with jobs and goals. Calyx has a plan, he has an outlook, and he has steps to achieve, and regardless of whether or not he's all that remains of Preservation or if he's just the head of an unnamed mass, he simply just had nothing to gain from shutting down Sphene's stasis and letting her die. Whether because of plans on the backburner, internal feelings about Real Sphene as the queen, or simply because it's more effort to make a move than it is to not, he just left her there and moved forward with his plans. That even if she is useless, sometimes you don't throw away useless things.

I'm honestly completely ignoring the chance that we'll learn more in the future here, simply because I don't know the future, I'm only speculating on what we have now. And with what we have now it almost boils down to a question of effort: if we accept Calyx's decisions to be the cold logic that he asserts them to be, which is more effort: killing her, or leaving her alive? And is the decision he made truly as driven by logic as he wants it to seem?